scholarly journals Geographic sharing of ribotype patterns in Enterococcus faecalis for bacterial source tracking

2007 ◽  
Vol 5 (4) ◽  
pp. 539-551 ◽  
Author(s):  
Peter G. Hartel ◽  
Robin L. Kuntz ◽  
Karen Rodgers ◽  
Samuel P. Myoda ◽  
Kerry J. Ritter ◽  
...  
Keyword(s):  
New York ◽  
Enterococcus Faecalis ◽  
Wastewater Treatment Plants ◽  
Geographic Distance ◽  
Similarity Index ◽  
Clonal Diversity ◽  
Mantel Test ◽  
Source Tracking ◽  
Tolerance Level ◽  
Bacterial Source Tracking

The limited host range of Enterococcus faecalis may reduce its clonal diversity and thereby increase its geographic sharing of ribotype patterns. Such sharing would be advantageous for bacterial source tracking (BST). We determined the geographic sharing of ribotype patterns in 752 Ent. faecalis isolates obtained primarily from wastewater treatment plants in Delaware (15 locations; 490 isolates), Georgia (2 locations; 48 isolates), Idaho (1 location; 118 isolates), New York (2 locations; 48 isolates), and Puerto Rico (2 locations; 48 isolates). Isolates were ribotyped with a RiboPrinter. When pooled across all locations and analyzed at a similarity index of 100% and a tolerance level of 1.00%, the 752 Ent. faecalis isolates yielded 652 different ribotypes, of which 429 (66%) were unshared. Even when the matching criterion was relaxed by decreasing the tolerance level from 1% to 10% or lowering the similarity cutoff from 100% to 90%, half or almost half of the ribotypes were unshared. A Mantel test of zero correlation showed no statistically significant correlation between ribotype patterns and geographic distance among the 32 samples (one location at one time) at either the 1.00% (P = 0.91) or 10.00% (P = 0.83) tolerance levels. Therefore, the percentage of ribotype patterns shared between two locations did not increase as the distance between locations decreased. In the case of BST, a permanent host origin database sufficiently large to encompass these ribotype patterns would be time-consuming and expensive to construct.

Targeted Sampling Protocol as Prelude to Bacterial Source Tracking with Enterococcus faecalis

2003 ◽  
Vol 32 (6) ◽  
pp. 2311-2318 ◽  
Author(s):  
Robin L. Kuntz ◽  
Peter G. Hartel ◽  
Dominique G. Godfrey ◽  
Jennifer L. McDonald ◽  
Keith W. Gates ◽  
...  
Keyword(s):  
Enterococcus Faecalis ◽  
Source Tracking ◽  
Sampling Protocol ◽  
Bacterial Source Tracking ◽  
Targeted Sampling

Presence of Enterococcus faecalis in broiler litter and wild bird feces for bacterial source tracking

2004 ◽  
Vol 38 (16) ◽  
pp. 3551-3557 ◽  
Author(s):  
Robin L. Kuntz ◽  
Peter G. Hartel ◽  
Karen Rodgers ◽  
William I. Segars
Keyword(s):  
Enterococcus Faecalis ◽  
Wild Bird ◽  
Source Tracking ◽  
Broiler Litter ◽  
Bacterial Source Tracking ◽  
Bird Feces

scholarly journals Genetic structure and dispersal patterns of the invasive psocid Liposcelis decolor (Pearman) in Australian grain storage systems

2010 ◽  
Vol 100 (5) ◽  
pp. 521-527 ◽  
Author(s):  
K.M. Mikac ◽  
N.N. FitzSimmons
Keyword(s):  
Genetic Structure ◽  
Isolation By Distance ◽  
Geographic Distance ◽  
Allelic Diversity ◽  
Mantel Test ◽  
Null Alleles ◽  
Dispersal Patterns ◽  
Long Distance ◽  
Population Comparisons ◽  
Low Levels

AbstractMicrosatellite markers were used to investigate the genetic structure among invasive L. decolor populations from Australia and a single international population from Kansas, USA to determine patterns of dispersal. Six variable microsatellites displayed an average of 2.5–4.2 alleles per locus per population. Observed (HO) heterozygosity ranged from 0.12–0.65 per locus within populations; but, in 13 of 36 tests, HO was less than expected. Despite low levels of allelic diversity, genetic structure estimated as θ was significant for all pairwise comparisons between populations (θ=0.05–0.23). Due to suspected null alleles at four loci, ENA (excluding null alleles) corrected FST estimates were calculated overall and for pairwise population comparisons. The ENA-corrected FST values (0.02–0.10) revealed significant overall genetic structure, but none of the pairwise values were significantly different from zero. A Mantel test of isolation by distance indicated no relationship between genetic structure and geographic distance among all populations (r2=0.12, P=0.18) and for Australian populations only (r2=0.19, P=0.44), suggesting that IBD does not describe the pattern of gene flow among populations. This study supports a hypothesis of long distance dispersal by L. decolor at moderate to potentially high levels.

Bacterial Source Tracking of Nonpoint Source Pollution Using GIS and DNA Fingerprinting Technologies

2011 ◽  
pp. 208-223
Author(s):  
M. E. Folkoff ◽  
E. A. Venso ◽  
D. W. Harris ◽  
M. F. Frana ◽  
M. S. Scott
Keyword(s):  
Water Pollution ◽  
Water Quality ◽  
Dna Fingerprinting ◽  
Physical Environment ◽  
Nonpoint Source ◽  
Point Sources ◽  
Source Tracking ◽  
Great Promise ◽  
Bacterial Source Tracking

This study is only the second to use DNA fingerprinting technology in Maryland to identify fecal coliform sources in order to guide the implementation of water pollution control practices in a watershed with bacterial impairment. By combining the use of digital air photos and GPS with GIS, fieldwork is planned and conducted more efficiently because sample sites can be selected that accurately represent the physical environment of the study area. We can also return to the field and find our sample sites or locate new ones, even in the remotest part of the study area. It is also possible to more accurately map the data directly in the context of its physical environment, greatly increasing the quality of analysis. The integration of DNA fingerprinting techniques with GIS shows great promise for extending our capabilities to identify the controls on water quality and point sources of waterborne health hazards.

scholarly journals Initial Mapping of the New York City Wastewater Virome

mSystems ◽  
2020 ◽  
Vol 5 (3) ◽  
Author(s):  
K. Gulino ◽  
J. Rahman ◽  
M. Badri ◽  
J. Morton ◽  
R. Bonneau ◽  
...  
Keyword(s):  
New York ◽  
New York City ◽  
York City ◽  
Wastewater Treatment Plants ◽  
Urban Environments ◽  
Metagenomic Data ◽  
Functional Importance ◽  
Wide Range ◽  
Viral Communities ◽  
Local Sampling

ABSTRACT Bacteriophages are abundant members of all microbiomes studied to date, influencing microbial communities through interactions with their bacterial hosts. Despite their functional importance and ubiquity, phages have been underexplored in urban environments compared to their bacterial counterparts. We profiled the viral communities in New York City (NYC) wastewater using metagenomic data collected in November 2014 from 14 wastewater treatment plants. We show that phages accounted for the largest viral component of the sewage samples and that specific virus communities were associated with local environmental conditions within boroughs. The vast majority of the virus sequences had no homology matches in public databases, forming an average of 1,700 unique virus clusters (putative genera). These new clusters contribute to elucidating the overwhelming proportion of data that frequently goes unidentified in viral metagenomic studies. We assigned potential hosts to these phages, which appear to infect a wide range of bacterial genera, often outside their presumed host. We determined that infection networks form a modular-nested pattern, indicating that phages include a range of host specificities, from generalists to specialists, with most interactions organized into distinct groups. We identified genes in viral contigs involved in carbon and sulfur cycling, suggesting functional importance of viruses in circulating pathways and gene functions in the wastewater environment. In addition, we identified virophage genes as well as a nearly complete novel virophage genome. These findings provide an understanding of phage abundance and diversity in NYC wastewater, previously uncharacterized, and further examine geographic patterns of phage-host association in urban environments. IMPORTANCE Wastewater is a rich source of microbial life and contains bacteria, viruses, and other microbes found in human waste as well as environmental runoff sources. As part of an effort to characterize the New York City wastewater metagenome, we profiled the viral community of sewage samples across all five boroughs of NYC and found that local sampling sites have unique sets of viruses. We focused on bacteriophages, or viruses of bacteria, to understand how they may influence the microbial ecology of this system. We identified several new clusters of phages and successfully associated them with bacterial hosts, providing insight into virus-host interactions in urban wastewater. This study provides a first look into the viral communities present across the wastewater system in NYC and points to their functional importance in this environment.

Application of PacBio Single Molecule Real-Time (SMRT) sequencing in bacterial source tracking analysis during milk powder production

Food Control ◽  
2018 ◽  
Vol 93 ◽  
pp. 226-234 ◽  
Author(s):  
Jicheng Wang ◽  
Yi Zheng ◽  
Xiaoxia Xi ◽  
Qiangchuan Hou ◽  
Haiyan Xu ◽  
...  
Keyword(s):  
Real Time ◽  
Single Molecule ◽  
Milk Powder ◽  
Source Tracking ◽  
Smrt Sequencing ◽  
Bacterial Source Tracking ◽  
Powder Production
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